Is it different in the digital version? Because whenever I looked it up for the card game basic/elite cards are only removed from the game when they are banished, not when they are returned to the box. By that ruling any cards you have extra in your deck after an adventure and any cards left over in locations that have not been permanently closed would not be removed from the game if they're basic or elite depending on what adventure you're on.
In that case passing on acquiring basic boons you don't want is beneficial as a way to remove it from the game, though this doesn't come up in any of the adventures currently available.